Related Experiment Video
Updated: Apr 26, 2026

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells
Published on: June 16, 2022
APADB: a database for alternative polyadenylation and microRNA regulation events
Sören Müller1, Lukas Rycak2, Fabian Afonso-Grunz1
1Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, GermanyPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany
Abstract:
Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3' end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3'UTR lengths, especially for chicken, and APADB provides necessary information to close this gap. Database URL: http://tools.genxpro.net/apadb/.
More Related Videos
11:00Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs
Published on: June 12, 2018
07:19Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells
Published on: September 28, 2011
Related Concept Videos
MicroRNAs
MicroRNAs
MicroRNAs
Regulation of Expression at Multiple Steps
Chromatin Structure Regulates pre-mRNA Processing
The chromatin structure, especially...
Experimental RNAi